LAMMPS (15 Jun 2020)
  using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP W-Be potential

# Initialize simulation

variable nsteps index 100
variable nrep equal 4
variable a equal 3.1803
units           metal

# generate the box and atom positions using a BCC lattice

variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4

boundary        p p p

lattice         bcc $a
lattice         bcc 3.1803
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
region          box block 0 ${nx} 0 ${ny} 0 ${nz}
region          box block 0 4 0 ${ny} 0 ${nz}
region          box block 0 4 0 4 0 ${nz}
region          box block 0 4 0 4 0 4
create_box      2 box
Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
  1 by 2 by 2 MPI processor grid
create_atoms    1 box
Created 128 atoms
  create_atoms CPU = 0.000 seconds
mass 1 183.84
mass 2 9.012182

set     group all type/fraction 2 0.05 3590153 # Change 5% of W to He
  5 settings made for type/fractiongroup   tungsten         type 1
123 atoms in group tungsten
group   beryllium        type 2
5 atoms in group beryllium
# choose potential

include WBe_Wood_PRB2019.snap
# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019)
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz1 equal 74
variable zblz2 equal 4

# Specify hybrid with SNAP and ZBL

pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 4.8 snap
pair_coeff 1 1 zbl ${zblz1} ${zblz1}
pair_coeff 1 1 zbl 74 ${zblz1}
pair_coeff 1 1 zbl 74 74
pair_coeff 1 2 zbl ${zblz1} ${zblz2}
pair_coeff 1 2 zbl 74 ${zblz2}
pair_coeff 1 2 zbl 74 4
pair_coeff 2 2 zbl ${zblz2} ${zblz2}
pair_coeff 2 2 zbl 4 ${zblz2}
pair_coeff 2 2 zbl 4 4
pair_coeff * * snap WBe_Wood_PRB2019.snapcoeff WBe_Wood_PRB2019.snapparam W Be
SNAP Element = W, Radius 0.5, Weight 1 
SNAP Element = Be, Radius 0.417932, Weight 0.959049 
SNAP keyword rcutfac 4.8123 
SNAP keyword twojmax 8 
SNAP keyword rfac0 0.99363 
SNAP keyword rmin0 0 
SNAP keyword bzeroflag 1 
SNAP keyword quadraticflag 0 


# Setup output

thermo          10
thermo_modify norm yes

# Set up NVE run

timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes

# Run MD

velocity all create 300.0 4928459 loop geom
fix 1 all nve
run             ${nsteps}
run             100
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 5.8123
  ghost atom cutoff = 5.8123
  binsize = 2.90615, bins = 5 5 5
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair zbl, perpetual, half/full from (2)
      attributes: half, newton on
      pair build: halffull/newton
      stencil: none
      bin: none
  (2) pair snap, perpetual
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.167 | 4.167 | 4.167 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0          300   -8.5980876            0   -8.5596125   -35284.855 
      10    296.32664   -8.5976164            0   -8.5596124   -35188.339 
      20    282.41417    -8.595832            0   -8.5596123   -34782.293 
      30    259.69014   -8.5929175            0   -8.5596121   -34113.316 
      40    230.50415   -8.5891741            0   -8.5596119   -33260.777 
      50    197.88816   -8.5849908            0   -8.5596116   -32309.975 
      60    165.27259   -8.5808076            0   -8.5596113   -31365.766 
      70    136.15697   -8.5770733            0   -8.5596111   -30542.657 
      80    113.58947   -8.5741788            0   -8.5596109    -29939.23 
      90    99.477916    -8.572369            0   -8.5596109   -29619.939 
     100    94.121939   -8.5716822            0    -8.559611   -29598.002 
Loop time of 0.668977 on 4 procs for 100 steps with 128 atoms

Performance: 6.458 ns/day, 3.717 hours/ns, 149.482 timesteps/s
97.2% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.57811    | 0.60637    | 0.63609    |   2.6 | 90.64
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.031571   | 0.061612   | 0.090021   |   8.3 |  9.21
Output  | 0.00015521 | 0.00021636 | 0.00038552 |   0.0 |  0.03
Modify  | 5.4836e-05 | 6.1393e-05 | 7.2956e-05 |   0.0 |  0.01
Other   |            | 0.0007139  |            |       |  0.11

Nlocal:    32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    431 ave 431 max 431 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    928 ave 928 max 928 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs:  1856 ave 1856 max 1856 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 7424
Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0

Total wall time: 0:00:00
